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    Smndc1 survival motor neuron domain containing 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 287768, updated on 2-May-2024

    Summary

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    Official Symbol
    Smndc1provided by RGD
    Official Full Name
    survival motor neuron domain containing 1provided by RGD
    Primary source
    RGD:1309151
    See related
    Ensembl:ENSRNOG00000014833 AllianceGenome:RGD:1309151
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable RNA binding activity. Predicted to be involved in RNA splicing; apoptotic process; and mRNA processing. Predicted to be located in Cajal body; cytoplasm; and nuclear speck. Predicted to be part of spliceosomal complex. Predicted to be active in nucleus. Orthologous to human SMNDC1 (survival motor neuron domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Kidney (RPKM 116.0), Thymus (RPKM 115.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Smndc1 in Genome Data Viewer
    Location:
    1q55
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (262395034..262406104, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (252389675..252400749, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (274096068..274107138, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134484110 Neighboring gene uncharacterized LOC108349710 Neighboring gene MAX interactor 1, dimerization protein Neighboring gene uncharacterized LOC103691375 Neighboring gene U2 spliceosomal RNA Neighboring gene uncharacterized LOC102551352

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Castello A, et al. Cell, 2012 Jun 8. PMID 22658674
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Clone Names

    • MGC112663

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Cajal body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    survival of motor neuron-related-splicing factor 30
    Names
    survival motor neuron domain-containing protein 1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001025400.3 → NP_001020571.1  survival of motor neuron-related-splicing factor 30

      See identical proteins and their annotated locations for NP_001020571.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      BC097986, BC098697, CB726049, CV106705
      UniProtKB/Swiss-Prot
      Q4KM88, Q4QQU6
      UniProtKB/TrEMBL
      A0A8L2UPB2, A6JHV2
      Related
      ENSRNOP00000068081.2, ENSRNOT00000076121.3
      Conserved Domains (1) summary
      cd20399
      Location:73 → 128
      Tudor_SPF30; Tudor domain found in survival of motor neuron-related-splicing factor 30 (SPF30) and similar proteins

    2. NM_001035234.2 → NP_001030311.1  survival of motor neuron-related-splicing factor 30

      See identical proteins and their annotated locations for NP_001030311.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the predominant transcript. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      BC098697, CB726049, CV106705, EV778425
      UniProtKB/Swiss-Prot
      Q4KM88, Q4QQU6
      UniProtKB/TrEMBL
      A0A8L2UPB2, A6JHV2
      Conserved Domains (1) summary
      cd20399
      Location:73 → 128
      Tudor_SPF30; Tudor domain found in survival of motor neuron-related-splicing factor 30 (SPF30) and similar proteins

    RNA

    1. NR_051995.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice junction compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC098697, CB726049, CV106705, EV778425
      Related
      ENSRNOT00000078670.2

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086019.1 Reference GRCr8

      Range
      262395034..262406104 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039102802.2 → XP_038958730.1  survival of motor neuron-related-splicing factor 30 isoform X1

      UniProtKB/Swiss-Prot
      Q4KM88, Q4QQU6
      UniProtKB/TrEMBL
      A0A8L2UPB2, A6JHV2
      Related
      ENSRNOP00000020539.5
      Conserved Domains (1) summary
      cd20399
      Location:73 → 128
      Tudor_SPF30; Tudor domain found in survival of motor neuron-related-splicing factor 30 (SPF30) and similar proteins

    2. XM_063282691.1 → XP_063138761.1  survival of motor neuron-related-splicing factor 30 isoform X2

    3. XM_063282693.1 → XP_063138763.1  survival of motor neuron-related-splicing factor 30 isoform X2

    4. XM_063282694.1 → XP_063138764.1  survival of motor neuron-related-splicing factor 30 isoform X3

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q4QQU6.1 GenPept UniProtKB/Swiss-Prot:Q4QQU6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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